Genome annotation with Braker3 1.0
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Run on GalaxyThis workflow uses Braker3 to annotate a genome.
Associated Tutorial
This workflows is part of the tutorial Genome annotation with Braker3, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Romane Libouban
Tutorial Author(s): Romane LIBOUBAN, Anthony Bretaudeau
Tutorial Contributor(s): Deepti Varshney, Saskia Hiltemann, Bérénice Batut
Grants(s): EuroScienceGateway
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Alignments from RNA-seq | Alignments from RNA-seq | Alignments from RNA-seq |
|
| BUSCO lineage | BUSCO lineage | BUSCO lineage |
|
| Genome sequence masked | Genome sequence masked | Genome sequence |
|
| Protein sequences | Protein sequences | Protein sequences |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Fasta Statistics | Fasta Statistics on the genome toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 |
| 5 | BUSCO on the genome sequences | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
| 6 | Braker3 | Genome annotation with Braker3 toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.8+galaxy0 |
| 7 | GFFRead | Converts GFF files to other formats, such as FASTA toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 |
| 8 | JBrowse | toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 |
| 9 | BUSCO on the predicted protein sequences | Completeness assessment of the genome using the Busco tool toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| fasta stats genome | fasta stats genome | n/a |
|
| busco table genome | busco table genome | n/a |
|
| busco sum genome | busco sum genome | n/a |
|
| busco image genome | busco image genome | n/a |
|
| busco missing genome | busco missing genome | n/a |
|
| busco gff genome | busco gff genome | n/a |
|
| braker gff | braker gff | n/a |
|
| predicted proteins | predicted proteins | n/a |
|
| jbrowse | jbrowse | n/a |
|
| busco image predicted proteins | busco image predicted proteins | n/a |
|
| busco gff predicted proteins | busco gff predicted proteins | n/a |
|
| busco sum predicted proteins | busco sum predicted proteins | n/a |
|
| busco missing predicted proteins | busco missing predicted proteins | n/a |
|
| busco table predicted proteins | busco table predicted proteins | n/a |
|
Version History
1.0
Creators and Submitter
Views: 1436 Downloads: 153 Runs: 1
Created: 2nd Jun 2025 at 10:56
Last updated: 28th Jul 2025 at 09:40
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